I have a Buriza-Do Kyanon that rolled with a 54% cooldown on vengeance. I have a dawn in the cube giving me 65%, however the game ignores the cubed dawn and uses the 54% from Buriza-Do Kyanon. The game should use the higher value of 65% cool down.
If you have the same item equipped and in the Cube, the value of the equipped item is used.
This has been the case since the Cube was introduced.
This is not a bug.